This class is an addition to the Unity Standard Asset Scripts (need to be imported in your project to get this gist working). This component can be used like the standard asset "First Person Controller", however it moves on the NavMesh (instead of colliders). This can save a lot of setup pain and performance.

NavMeshPlayerMovement.cs

using System;
using UnityEngine;
using UnityEngine.AI;
using UnityStandardAssets.Characters.FirstPerson;
using UnityStandardAssets.CrossPlatformInput;

namespace ZKW.PlayerMovement
{
    public class NavMeshPlayerMovement : MonoBehaviour
    {
        private const string noPlayerNavmeshCheckTag = "No Player NavMesh Check";

        public Camera cam;

        private float yWhileInNoCheckArea;

        private bool isInNoCheckArea;
        public MouseLook mouseLook = new MouseLook();
        public MovementSettings movementSettings = new MovementSettings();


        private Transform myTranform;


        public bool Running
        {
            get
            {
#if !MOBILE_INPUT
                return movementSettings.Running;
#else
				return false;
#endif
            }
        }


        private void Start()
        {
            myTranform = transform;
            mouseLook.Init(myTranform, cam.transform);
        }


        private void Update()
        {
            RotateView();

            var input = GetInput();

            if (!(Mathf.Abs(input.x) > float.Epsilon) && !(Mathf.Abs(input.y) > float.Epsilon)) return;

            // always move along the camera forward as it is the direction that it being aimed at
            var desiredMove = cam.transform.forward*input.y + cam.transform.right*input.x;
            desiredMove = Vector3.ProjectOnPlane(desiredMove, Vector3.zero).normalized;

            desiredMove.x = desiredMove.x*movementSettings.CurrentTargetSpeed;
            desiredMove.z = desiredMove.z*movementSettings.CurrentTargetSpeed;
            desiredMove.y = desiredMove.y*movementSettings.CurrentTargetSpeed;

            var movement = desiredMove*Time.deltaTime;

            if (movement.magnitude == 0) return;

            var currPos = myTranform.position;
            var desiredPos = currPos + movement;

            if (isInNoCheckArea)
                desiredPos.y = yWhileInNoCheckArea;

            myTranform.position = desiredPos;

            if (isInNoCheckArea) return;

            movePlayerToNearestNavMeshPosition(desiredPos);
        }

        private void movePlayerToNearestNavMeshPosition(Vector3 curr)
        {
            var distance = 0.01f;
            var hit = new NavMeshHit();
            do
            {
                NavMesh.SamplePosition(curr, out hit, distance, NavMesh.AllAreas);
                distance *= 2f;
            } while (!hit.hit);

            myTranform.position = hit.position;
        }

        private void OnTriggerEnter(Collider other)
        {
            if (other.tag != noPlayerNavmeshCheckTag) return;

            isInNoCheckArea = true;
            yWhileInNoCheckArea = myTranform.position.y;
        }

        private void OnTriggerExit(Collider other)
        {
            if (other.tag == noPlayerNavmeshCheckTag)
                isInNoCheckArea = false;
        }

        private Vector2 GetInput()
        {
            var input = new Vector2
            {
                x = CrossPlatformInputManager.GetAxis("Horizontal"),
                y = CrossPlatformInputManager.GetAxis("Vertical")
            };
            movementSettings.UpdateDesiredTargetSpeed(input);
            return input;
        }

        private void RotateView()
        {
            //avoids the mouse looking if the game is effectively paused
            if (Mathf.Abs(Time.timeScale) < float.Epsilon) return;

            // get the rotation before it's changed
            mouseLook.LookRotation(transform, cam.transform);
        }

        [Serializable]
        public class MovementSettings
        {
            public float BackwardSpeed = 4.0f; // Speed when walking backwards

            [HideInInspector] public float CurrentTargetSpeed = 8f;

            public float ForwardSpeed = 8.0f; // Speed when walking forward
            public float JumpForce = 30f;

#if !MOBILE_INPUT
#endif
            public KeyCode RunKey = KeyCode.LeftShift;
            public float RunMultiplier = 2.0f; // Speed when sprinting

            public float StrafeSpeed = 4.0f; // Speed when walking sideways

#if !MOBILE_INPUT
            public bool Running { get; private set; }
#endif

            public void UpdateDesiredTargetSpeed(Vector2 input)
            {
                if (input == Vector2.zero) return;
                if ((input.x > 0) || (input.x < 0))
                    CurrentTargetSpeed = StrafeSpeed;
                if (input.y < 0)
                    CurrentTargetSpeed = BackwardSpeed;
                if (input.y > 0)
                    CurrentTargetSpeed = ForwardSpeed;
#if !MOBILE_INPUT
                if (Input.GetKey(RunKey))
                {
                    CurrentTargetSpeed *= RunMultiplier;
                    Running = true;
                }
                else
                {
                    Running = false;
                }
#endif
            }
        }
    }
}